Transparency in Blender 2.8 GPU Python Module
So I found the answer to this one with some help from the folks on Blender.chat (thanks Okuma_10!).

In your draw method before you draw put in: -

glEnable(GL_BLEND)


and after you're done drawing put in: -

glDisable(GL_BLEND)


also make sure you import all of BGL with: -

from bgl import *


Apparently there is no performance cost for doing so as the program naturally iterates through the entire library anyway. After that the alpha values should work.